Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: CNTools
https://packages.ecosyste.ms/registries/bioconductor.org/packages/CNTools
Convert segment data into a region by sample matrix to allow for other high level computational analyses.
1 version
Latest release: about 1 year ago
1 dependent package
53,629 downloads total
Papers Mentioning CNTools 21
10.18632/oncotarget.22928
Comparing the genomes of cutaneous melanoma tumors to commercially available cell linesCited by: 10
Author(s): Stephen A. Luebker, Weiwei Zhang, Scott A. Koepsell
Software Mentions: 11
Published: almost 7 years ago
10.1371/journal.pone.0183517
Integrated analysis of long non-coding RNAs in human gastric cancer: An in silico studyCited by: 7
Author(s): Han Wang, Zhenyu Zhang, Bangshun He, Yu Xu, Jun Zhang, Weijun Cao
Software Mentions: 6
Published: about 7 years ago
10.1186/s13059-020-02175-0
Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticityCited by: 32
Author(s): Won‐Chul Lee, Alexandre Reuben, Xin Hu, Nicholas McGranahan, Runzhe Chen, Ali Jalali, Marcelo V. Negrão, Shawna M. Hubert, Chad Tang, Chia-Chin Wu, Anthony San Lucas, Whijae Roh, Kenichi Suda, Jihye Kim, Aik-Choon Tan, David H. Peng, Wei Lü, Ximing Tang, Chi-Wan Chow, Junya Fujimoto, Carmen Behrens, Neda Kalhor, Kazutaka Fukumura, Marcus Coyle, Rebecca Thornton, Curtis Gumbs, Jun Li, Chang-Jiun Wu, Latasha Little, Emily Roarty, Xingzhi Song, J. Jack Lee, Erik P. Sulman, Ganesh Rao, Stephen G. Swisher, Lixia Diao, Jing Wang, John V. Heymach, Jason T. Huse, Paul Scheet, Ignacio I. Wistuba, Don L. Gibbons, P. Andrew Futreal, Jianhua Zhang, Daniel R. Gomez, Jianjun Zhang
Software Mentions: 5
Published: about 4 years ago
10.3389/fonc.2020.00444
Multi-Omics Integration Reveals a Competitive Endogenous RNAs Network for the Identification of Progression Biomarkers and the Stratification of Patients Diagnosed With NephroblastomaCited by: 2
Author(s): Jingbo Wang, Yuan Wang, Han Liang, Mohamed Shahen, Chaofeng Hu, Furong Li
Software Mentions: 5
Published: over 4 years ago
10.1038/srep18616
Developmental genes significantly afflicted by aberrant promoter methylation and somatic mutation predict overall survival of late-stage colorectal cancerCited by: 15
Author(s): Ning An, Xue Yang, Shujun Cheng, Guiqi Wang, Kaitai Zhang
Software Mentions: 4
Published: almost 9 years ago
10.1371/journal.pgen.1008558
Autophagy gene haploinsufficiency drives chromosome instability, increases migration, and promotes early ovarian tumorsCited by: 28
Author(s): Joe R. Delaney, C. A. Patel, Jaidev Bapat, Christian M. Jones, Maria Ramos-Zapatero, Katherine K. Ortell, Ralph Tanios, Mina Haghighiabyaneh, Joshua Axelrod, John W. DeStefano, Isabelle Tancioni, David D. Schlaepfer, Olivier Harismendy, Albert R. La Spada, Dwayne G. Stupack
Software Mentions: 4
Published: almost 5 years ago
10.1186/s12885-021-08777-6
ER expression associates with poor prognosis in male lung squamous carcinoma after radical resectionCited by: 2
Author(s): Xue Yang, Xiangfeng Jin, Rongjian Xu, Zhuang Yu, Ning An
Software Mentions: 3
Published: about 3 years ago
10.1371/journal.pone.0056274
Headbobber: A Combined Morphogenetic and Cochleosaccular Mouse Model to Study 10qter Deletions in Human DeafnessCited by: 7
Author(s): Annalisa Buniello, Rachel E. Hardisty-Hughes, Johanna Pass, Eva Bober, Richard J.H. Smith, Karen P. Steel
Software Mentions: 3
Published: almost 12 years ago
10.1186/s13073-021-00958-z
Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8Cited by: 6
Author(s): Giwon Shin, Stephanie Greer, Erik Hopmans, Susan M. Grimes, HoJoon Lee, Liang Zhao, Laura Miotke, Carlos J. Suarez, Alison Almeda, Sigurdís Haraldsdóttir, Hanlee P. Ji
Software Mentions: 3
Published: about 3 years ago
10.1038/sdata.2018.240
Meta-mining of copy number profiles of high-risk neuroblastoma tumorsCited by: 26
Author(s): Pauline Depuydt, Jan Koster, Valentina Boeva, Toby Dylan Hocking, Frank Speleman, Gudrun Schleiermacher, Katleen De Preter
Software Mentions: 3
Published: about 6 years ago
10.1038/srep42060
Integrative analysis of copy number and transcriptional expression profiles in esophageal cancer to identify a novel driver gene for therapyCited by: 26
Author(s): Gaochao Dong, Qixing Mao, Decai Yu, Yi Zhang, Mantang Qiu, Gaoyue Dong, Qiang Chen, Wenjie Xia, Jie Wang, Lin Xu, Feng Jiang
Software Mentions: 3
Published: almost 8 years ago
10.18632/oncotarget.16178
Survival differences of CIMP subtypes integrated with CNA information in human breast cancerCited by: 3
Author(s): Huihan Wang, Weili Yan, Shumei Zhang, Yue Gu, Yihan Wang, Yanjun Wei, Hongbo Liu, Fang Wang, Qiong Wu, Yan Zhang
Software Mentions: 3
Published: over 7 years ago
10.1038/s41598-018-22126-x
A validation and extended description of the Lund taxonomy for urothelial carcinoma using the TCGA cohortCited by: 118
Author(s): Nour Al Dain Marzouka, Pontus Eriksson, Carlos Rovira, Fredrik Liedberg, Gottfrid Sjödahl, Mattias Höglund
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0203007
Genomic region detection via Spatial Convex ClusteringCited by: 2
Author(s): John Nagorski, Genevera I. Allen
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pgen.1004751
Notch3 Interactome Analysis Identified WWP2 as a Negative Regulator of Notch3 Signaling in Ovarian CancerCited by: 60
Author(s): Jin Myung Jung, Alexander Stoeck, Bin Guan, Ren‐Chin Wu, Heng Zhu, Seth Blackshaw, Ie Ming Shih, Tian Li Wang
Software Mentions: 2
Published: about 10 years ago
10.1371/journal.pone.0041055
A Global View of the Oncogenic Landscape in Nasopharyngeal Carcinoma: An Integrated Analysis at the Genetic and Expression LevelsCited by: 45
Author(s): Chunfang Hu, Wenbin Wei, Xiaoyi Chen, Ciarán Woodman, Yunhong Yao, John M. Nicholls, Irène Joab, Sim K. Sihota, Jian Yong Shao, Khadidja Derkaoui, Aicha Amari, Stephanie Louise Maloney, Andrew I. Bell, Paul G. Murray, Christopher W. Dawson, Young Lw, John R. Arrand
Software Mentions: 1
Published: over 12 years ago
10.1186/s12864-016-2911-z
Comprehensive comparison of molecular portraits between cell lines and tumors in breast cancerCited by: 151
Author(s): Guanglong Jiang, Shijun Zhang, Aida Yazdanparast, Meng Li, Aniruddha Pawar, Yunlong Liu, Sai Mounika Inavolu, Lijun Cheng
Software Mentions: 1
Published: over 8 years ago
10.1155/2015/901303
Deciphering the Correlation between Breast Tumor Samples and Cell Lines by Integrating Copy Number Changes and Gene Expression ProfilesCited by: 10
Author(s): Yi Sun, Qi Liu
Software Mentions: 1
Published: almost 10 years ago
10.15252/msb.20145216
Measuring error rates in genomic perturbation screens: gold standards for human functional genomicsCited by: 312
Author(s): Traver Hart, Kevin R. Brown, Fabrice Sircoulomb, Robert Rottapel, Jason Moffat
Software Mentions: 1
Published: over 10 years ago
10.18632/oncotarget.14018
Identifying the clonal origin of synchronous multifocal tumors in the hepatobiliary and pancreatic system using multi-omic platformsCited by: 9
Author(s): Weiqin Jiang, Yongfeng Ding, Yifei Shen, Longjiang Fan, Linfu Zhou, Zhi Li, Yi Zheng, Peng Zhao, Lulu Liu, Zhou Tong, Weijia Fang, Weilin Wang
Software Mentions: 1
Published: almost 8 years ago
10.1186/s12920-020-00736-7
Constructing cancer patient-specific and group-specific gene networks with multi-omics dataCited by: 10
Author(s): Wook Lee, De-Shuang Huang, Kyungsook Han
Software Mentions: 1
Published: over 4 years ago